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1.
Int J Syst Evol Microbiol ; 64(Pt 5): 1488-1494, 2014 May.
Article in English | MEDLINE | ID: mdl-24453232

ABSTRACT

Two Gram-staining-negative, strictly aerobic, non-endospore-forming, non-motile, rod-shaped bacteria, designated strains YIT 12745T and YIT 12746T, were isolated from sludge from a wastewater treatment plant. 16S rRNA gene sequence analyses indicated that these strains belonged to the genus Flavobacterium. In these analyses, strains YIT 12745T and YIT 12746T were most closely related to the type strains of Flavobacterium caeni and Flavobacterium terrigena, with 16S rRNA gene sequence similarity values of 94.9% and 96.2%, respectively. For both novel strains, menaquinone (MK-6) was the only respiratory quinone. The major fatty acids of strain YIT 12745T were iso-C15:1 G (14.4%), iso-C16:0 (13.2%), C15:0 (12.9%), iso-C15:0 (12.9%) and iso-C17:0 3-OH (11.5%). Those of strain YIT 12746T were iso-C15:0 (21.5%), iso-C16:0 (13.3%), C15:0 (12.0%) and iso-C15:1 G (11.9%). The genomic DNA G+C contents of strains YIT 12745T and YIT 12746T were 48.7 and 30.9 mol%, respectively. From their differential phenotypic and phylogenetic characteristics, these strains are considered to represent two novel species of the genus Flavobacterium, for which the names Flavobacterium longum sp. nov. (type strain YIT 12745T=JCM 19141T=DSM 27077T) and Flavobacterium urocaniciphilum sp. nov. (type strain YIT 12746T=JCM 19142T=DSM 27078T) are proposed. Emended descriptions of Flavobacterium caeni and Flavobacterium terrigena are also proposed.


Subject(s)
Flavobacterium/classification , Phylogeny , Sewage/microbiology , Wastewater/microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Flavobacterium/genetics , Flavobacterium/isolation & purification , Japan , Molecular Sequence Data , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
2.
Microbiol Immunol ; 56(3): 195-7, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22469182

ABSTRACT

Succinatimonas hippei is a new bacterial species isolated from human feces. Here we report that the growth of S. hippei YIT 12066(T) depends on CO(2) or bicarbonate and the headspace gas produced by microbiota. Genetic defect for carbonic anhydrase in this bacterium suggested a reason for the syntrophic property of CO(2) dependency and may suggest an adaptation to its habitat.


Subject(s)
Carbon Dioxide/metabolism , Feces/microbiology , Succinivibrionaceae/growth & development , Succinivibrionaceae/metabolism , Bicarbonates/metabolism , Carbonic Anhydrases/deficiency , Humans , Succinivibrionaceae/enzymology , Succinivibrionaceae/isolation & purification
3.
Appl Environ Microbiol ; 78(2): 511-8, 2012 Jan.
Article in English | MEDLINE | ID: mdl-22081579

ABSTRACT

Isolation, cultivation, and characterization of the intestinal microorganisms are important for understanding the comprehensive physiology of the human gastrointestinal (GI) tract microbiota. Here, we isolated two novel bacterial strains, YIT 12067(T) and YIT 12068, from the feces of healthy human adults. Phylogenetic analysis indicated that they belonged to the same species and were most closely related to Phascolarctobacterium faecium ACM 3679(T), with 91.4% to 91.5% 16S rRNA gene sequence similarities, respectively. Substrate availability tests revealed that the isolates used only succinate; they did not ferment any other short-chain fatty acids or carbohydrates tested. When these strains were cocultured with the xylan-utilizing and succinate-producing bacterium Paraprevotella xylaniphila YIT 11841(T), in medium supplemented with xylan but not succinate, their cell numbers became 2 to 3 orders of magnitude higher than those of the monoculture; succinate became undetectable, and propionate was formed. Database analysis revealed that over 200 uncultured bacterial clones from the feces of humans and other mammals showed high sequence identity (>98.7%) to YIT 12067(T). Real-time PCR analysis also revealed that YIT 12067(T)-like bacteria were present in 21% of human fecal samples, at an average level of 3.34 × 10(8) cells/g feces. These results indicate that YIT 12067(T)-like bacteria are distributed broadly in the GI tract as subdominant members that may adapt to the intestinal environment by specializing to utilize the succinate generated by other bacterial species. The phylogenetic and physiological properties of YIT 12067(T) and YIT 12068 suggest that these strains represent a novel species, which we have designated Phascolarctobacterium succinatutens sp. nov.


Subject(s)
Feces/microbiology , Succinic Acid/metabolism , Veillonellaceae/classification , Veillonellaceae/isolation & purification , Bacterial Typing Techniques , Cluster Analysis , Culture Media/chemistry , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Humans , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Veillonellaceae/genetics , Veillonellaceae/metabolism
4.
Int J Syst Evol Microbiol ; 62(Pt 1): 144-149, 2012 Jan.
Article in English | MEDLINE | ID: mdl-21357455

ABSTRACT

A novel, strictly anaerobic, non-motile, non-spore-forming, Gram-negative, short, straight rod with tapered ends, designated YIT 12065(T), was isolated from human faeces. Strain YIT 12065(T) was saccharolytic and negative for catalase, oxidase and urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. The end products of glucose fermentation were acetic acid and a small amount of butyric acid. The DNA G+C content was 51.3 mol%. The predominant fatty acids were iso-C(15:0), C(16:0) and C(14:0). Respiratory quinones were not detected. The cell wall contained glutamic acid, serine, alanine and ll-diaminopimelic acid. The whole-cell sugars were ribose, rhamnose, galactose and glucose. Phylogenetic analyses based on 16S rRNA gene sequences using three treeing algorithms revealed that the strain formed a novel family-level lineage within the phylum Firmicutes, class Clostridia, order Clostridiales. Caldicoprobacter oshimai JW/HY-331(T) was shown to be the closest named relative on the basis of 16S rRNA gene sequence similarity (86.9%), followed by Tindallia californiensis DSM 14871(T) (86.3%) and Clostridium ganghwense JCM 13193(T) (86.1%). Similar 16S rRNA gene sequences (98.6-96.7%) were found amongst faecal uncultured clones of human and dugong (Dugong dugon). They clustered with strain YIT 12065(T) in a distinct and deep evolutionary lineage of descent in the order Clostridiales. The distinct phylogenetic position supports the proposal of Christensenella gen. nov., with the type species Christensenella minuta sp. nov. (type strain YIT 12065(T) =DSM 22607(T) =JCM 16072(T)). A new family Christensenellaceae fam. nov. is also proposed.


Subject(s)
Feces/microbiology , Gram-Positive Bacteria/classification , Gram-Positive Bacteria/isolation & purification , Acetic Acid/metabolism , Anaerobiosis , Bacterial Typing Techniques , Base Composition , Butyrates/metabolism , Carbohydrates/analysis , Catalase/metabolism , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/metabolism , Fermentation , Glucose/metabolism , Gram-Positive Bacteria/genetics , Gram-Positive Bacteria/physiology , Humans , Molecular Sequence Data , Oxidoreductases/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Sucrose/metabolism , Urease/metabolism
5.
Int J Syst Evol Microbiol ; 61(Pt 3): 637-643, 2011 Mar.
Article in English | MEDLINE | ID: mdl-20400667

ABSTRACT

A novel, strictly anaerobic, non-spore-forming, Gram-reaction-negative coccobacillus bacterium, designated strain YIT 12071(T), was isolated from human faeces. Biochemically, this strain was largely unreactive and asaccharolytic. Growth of this strain in peptone-yeast-extract broth was weak, producing no visible turbidity, and no short-chain fatty acids were detected as an end product of metabolism. Following 16S rRNA gene sequence analysis, strain YIT 12071(T) was found to be most closely related to Parasutterella excrementihominis (90  % sequence similarity) and phylogenetically distinct from other known genera belonging to the order Burkholderiales. Biochemical data supported the affiliation of this strain with the genus Parasutterella. Strain YIT 12071(T), therefore, represents a novel species of the genus Parasutterella, for which the name Parasutterella secunda sp. nov. is proposed. The type strain is YIT 12071(T) (=DSM 22575(T) =JCM 16078(T)). On the basis of 16S rRNA gene sequence analysis, species of the genera Sutterella and Parasutterella form a distinct and deep evolutionary lineage of descent in the order Burkholderiales. This lineage could not be associated with any of the four known families of the order Burkholderiales. The distinct phylogenetic position and the unusual combination of chemotaxonomic characteristics shared by these genera, such as the predominant quinones and cellular fatty acid compositions, suggest that they constitute a novel family in the order Burkholderiales, for which the name Sutterellaceae fam. nov. is proposed to accommodate the genera Sutterella and Parasutterella.


Subject(s)
Betaproteobacteria/classification , Betaproteobacteria/isolation & purification , Feces/microbiology , Bacterial Typing Techniques , Betaproteobacteria/genetics , Betaproteobacteria/physiology , Cluster Analysis , Culture Media/chemistry , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/analysis , Humans , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
6.
Int J Syst Evol Microbiol ; 60(Pt 6): 1296-1302, 2010 Jun.
Article in English | MEDLINE | ID: mdl-19667375

ABSTRACT

Two anaerobic, non-spore-forming, non-motile, Gram-negative-staining bacteria, strains YIT 12060(T) and YIT 12061(T), were isolated from human faeces. Cells of strain YIT 12060(T) were coccoid to rod-shaped with round ends, positive for catalase, negative for indole and oxidase production, produced succinic and acetic acids as end products of glucose metabolism in peptone/yeast extract/glucose medium and had a DNA G+C content of 55.2 mol%. The main respiratory quinones were MK-10 (40%) and MK-11 (57%). Fatty acid analysis demonstrated the presence of a high concentration of iso-C(15 : 0) (56%). Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to species of the genus Alistipes, with 90.9-92.6% gene sequence similarities to type strains of this species. Phylogenetic analysis and biochemical data supported the affiliation of strain YIT 12060(T) to the genus Alistipes of the family 'Rikenellaceae'. Strain YIT 12060(T) therefore represents a novel species of the genus Alistipes for which the name Alistipes indistinctus sp. nov. is proposed; the type strain is YIT 12060(T) (=DSM 22520(T)=JCM 16068(T)). Cells of the other isolate, strain YIT 12061(T), were pleomorphic rods that were asaccharolytic, catalase- and oxidase-negative, positive for gelatin hydrolysis and indole production, produced small amounts of succinic, acetic and iso-valeric acids as end products of metabolism in peptone/yeast extract medium and had a DNA G+C content of approximately 42.4 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family 'Porphyromonadaceae' and related to the type strains of Odoribacter splanchnicus (89.6%) and Odoribacter denticanis (86.2%); similarity values with strains of recognized species within the family 'Porphyromonadaceae' were less than 84 %. Biochemical data supported the affiliation of strain YIT 12061(T) to the genus Odoribacter. Strain YIT 12061(T) therefore represents a novel species for which the name Odoribacter laneus sp. nov. is proposed; the type strain is YIT 12061(T) (=DSM 22474(T)=JCM 16069(T)).


Subject(s)
Bacteroidetes/isolation & purification , Feces/microbiology , Adult , Bacteroidetes/classification , Bacteroidetes/genetics , Bacteroidetes/metabolism , Catalase/metabolism , Fatty Acids/analysis , Humans , Male , Middle Aged , Molecular Sequence Data , Phylogeny
7.
Int J Syst Evol Microbiol ; 60(Pt 8): 1864-1869, 2010 Aug.
Article in English | MEDLINE | ID: mdl-19767355

ABSTRACT

Three Gram-stain-negative, obligately anaerobic, non-spore-forming, rod-shaped bacteria (strains YIT 12056T, YIT 12057T and YIT 12058T) were isolated from human faeces. These strains were characterized by phylogenetic analyses based on 16S rRNA gene sequence and phenotypic tests. 16S rRNA gene sequence analyses revealed that strains YIT 12056T, YIT 12057T and YIT 12058T were most closely related to the type strains of Bacteroides gallinarum, Bacteroides uniformis and Bacteroides intestinalis with approximate similarity values of 96.6, 95.0 and 96.7%, respectively. The DNA G+C contents of the novel strains were 45.3 (YIT 12056T), 45.2 (YIT 12057T) and 43.6 mol% (YIT 12058T) and the major respiratory quinones of all three isolates were menaquinones MK-10 and MK-11. These properties were typical for members of the genus Bacteroides. The results of the other phenotypic analyses also supported the affiliation of these strains to the genus Bacteroides. The 16S rRNA gene sequence analysis, analysis of the major cellular fatty acids and other biochemical tests enabled the genotypic and phenotypic differentiation of the three new strains. Based on these data, three novel species, Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov. are proposed. The type strains of B. clarus, B. fluxus and B. oleiciplenus are YIT 12056T (=JCM 16067T=DSM 22519T), YIT 12057T (=JCM 16101T=DSM 22534T) and YIT 12058T (=JCM 16102T=DSM 22535T), respectively.


Subject(s)
Bacteroides/classification , Bacteroides/isolation & purification , Feces/microbiology , Bacteroides/genetics , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , Humans , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics
8.
Int J Syst Evol Microbiol ; 60(Pt 11): 2639-2646, 2010 Nov.
Article in English | MEDLINE | ID: mdl-20023061

ABSTRACT

Three Gram-positive, strictly anaerobic, non-spore-forming, rod-shaped organisms (strains YIT 12062(T), YIT 12063(T) and YIT 12064) were isolated from human faeces. Strain YIT 12062(T) was asaccharolytic and possessed a DNA G+C content of 58.3 mol%. Cells of strain YIT 12062(T) were negative for catalase, oxidase, urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. Based on 16S rRNA gene sequence analysis, strain YIT 12062(T) was assigned to the genus Slackia (91.7-96.0 % sequence similarities to type strains of Slackia species). Biochemical data showed that the isolate was phenotypically distinct from all recognized species of the genus Slackia. Strain YIT 12062(T) therefore represents a novel species in the genus Slackia, for which the name Slackia piriformis sp. nov. is proposed. The type strain is YIT 12062(T) (=DSM 22477(T)=JCM 16070(T)). Following 16S rRNA gene sequence analysis, strains YIT 12063(T) and YIT 12064, which were isolated from different subjects, were shown to be most closely related to species of the genus Collinsella (93.8-95.1 % similarities to type strains). Although their phenotypic characteristics were very similar and they shared >99 % 16S rRNA gene sequence similarity and >97±1.8 % DNA-DNA relatedness, the two isolates could be discriminated by RAPD fingerprints. The DNA G+C contents of strains YIT 12063(T) and YIT 12064 were 60.8 and 61.0 mol%, respectively. They were saccharolytic in API test systems, positive for aesculin hydrolysis and negative for catalase, oxidase, urease, indole production, nitrate reduction and gelatin hydrolysis. The major end products of glucose fermentation of these strains were lactate, acetate and formate. Biochemical data supported the affiliation of strains YIT 12063(T) and YIT 12064 to the genus Collinsella and showed that they were phenotypically distinct from all recognized species of the genus Collinsella. Strains YIT 12063(T) and YIT 12064 therefore represent a novel species of the genus Collinsella, for which the name Collinsella tanakaei sp. nov. is proposed. The type strain is YIT 12063(T) (=DSM 22478(T)=JCM 16071(T)).


Subject(s)
Actinobacteria/classification , Actinobacteria/isolation & purification , Feces/microbiology , Actinobacteria/enzymology , Actinobacteria/genetics , Adult , Bacterial Proteins/metabolism , Base Composition , Catalase/metabolism , DNA, Bacterial/genetics , Humans , Male , Middle Aged , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Urease/metabolism
9.
Int J Syst Evol Microbiol ; 60(Pt 8): 1788-1793, 2010 Aug.
Article in English | MEDLINE | ID: mdl-19749029

ABSTRACT

A novel strictly anaerobic, non-spore-forming, non-motile, non-flagellated, rod-shaped, Gram-negative bacterium (YIT 12066T) was isolated from human faeces. The isolate was negative for catalase, oxidase, urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. The major end products of glucose metabolism were succinate and acetate. The major cellular fatty acids (>10%) were C14:0, C18:1omega7c, C18:1omega9c, C16:1omega7c and C16:0. The G+C content of the DNA was 40.3 mol%. 16S rRNA gene sequence analysis showed that strain YIT 12066T was most closely related to members of the family Succinivibrionaceae, with sequence similarity of 92-87%. However, some phenotypic characteristics such as cellular morphology and the major fatty acid profile of strain YIT 12066T were markedly different from those of other members of the family Succinivibrionaceae. On the basis of both phylogenetic and phenotypic evidence, it is suggested that strain YIT 12066T represents a novel species in a new genus, for which the name Succinatimonas hippei gen. nov., sp. nov. is proposed; the type strain of Succinatimonas hippei is YIT 12066T (=DSM 22608T =JCM 16073T).


Subject(s)
Feces/microbiology , Gammaproteobacteria/classification , Gammaproteobacteria/isolation & purification , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , Fatty Acids/metabolism , Gammaproteobacteria/genetics , Gammaproteobacteria/metabolism , Humans , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics
10.
Int J Syst Evol Microbiol ; 59(Pt 8): 1895-900, 2009 Aug.
Article in English | MEDLINE | ID: mdl-19567577

ABSTRACT

Two anaerobic, non-spore-forming, pleomorphic, Gram-negative rods, designated YIT 11840T and YIT 11841T, were isolated from human faeces. The organisms were catalase-negative, produced succinic and acetic acids as end products of glucose metabolism and had DNA G+C contents of approximately 48-49 mol%. Although the phenotypic characteristics of these two strains were very similar, analysis of their 16S rRNA gene sequences showed that they are only distantly related (93.8%), indicating that they represent two different species. A comparative sequence analysis revealed that these two species are members of the family 'Prevotellaceae' but are phylogenetically distant (<88% sequence similarity) from the known genera belonging to this family, including Prevotella, Hallela and Xylanibacter. On the basis of the phylogenetic analysis and physiological tests, strains YIT 11840T and YIT 11841T represent two novel species of a new genus, for which the names Paraprevotella clara gen. nov., sp. nov. (type strain YIT 11840T=JCM 14859T=DSM 19731T), the type species, and Paraprevotella xylaniphila sp. nov. (type strain YIT 11841T=JCM 14860T=DSM 19681T) are proposed.


Subject(s)
Feces/microbiology , Prevotella/classification , Prevotella/isolation & purification , Acetic Acid/metabolism , Anaerobiosis , Bacterial Typing Techniques , Base Composition , Catalase/metabolism , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Humans , Molecular Sequence Data , Phylogeny , Prevotella/genetics , Prevotella/physiology , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Succinic Acid/metabolism
11.
Int J Syst Evol Microbiol ; 59(Pt 7): 1793-7, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19542131

ABSTRACT

A novel, strictly anaerobic, non-spore-forming, Gram-negative coccobacillus (strain YIT 11859(T)) was isolated from human faeces. Biochemically, this strain was largely unreactive and was asaccharolytic. Growth of strain YIT 11859(T) in peptone-yeast extract broth produced no visible turbidity, and a trace amount of propionate was detected as an end product of metabolism. 16S rRNA gene sequence analysis showed that strain YIT 11859(T) was related most closely to the type strains of Sutterella species, with 90.8-88.0 % sequence similarity. Phylogenetic analysis of these and other related sequences confirmed that strain YIT 11859(T) was phylogenetically most closely associated with Sutterella species, but formed a separate cluster, indicating that strain YIT 11859(T) represents a novel member of the family Alcaligenaceae. Fatty acid analysis demonstrated the presence of a high concentration of C(18 : 1)omega9c (75 % of the total). The main respiratory quinones were menaquinone (MK-6) and methylated menaquinone (MMK-6). The G+C content of the DNA was 49.8 mol%. These results suggest that strain YIT 11859(T) represents a novel species of a new genus, for which the name Parasutterella excrementihominis gen. nov., sp. nov. is proposed. The type strain of Parasutterella excrementihominis is YIT 11859(T) (=DSM 21040(T) =JCM 15078(T)).


Subject(s)
Alcaligenaceae/classification , Feces/microbiology , Alcaligenaceae/genetics , Alcaligenaceae/isolation & purification , Alcaligenaceae/physiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/analysis , Fatty Acids/analysis , Genes, rRNA , Genotype , Humans , Japan , Molecular Sequence Data , Phenotype , Phylogeny , Quinones/analysis , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Species Specificity
12.
Int J Syst Evol Microbiol ; 58(Pt 12): 2716-20, 2008 Dec.
Article in English | MEDLINE | ID: mdl-19060046

ABSTRACT

Two anaerobic, non-spore-forming, bacteria (YIT 11850(T) and YIT 11860(T)) that stained Gram-negative, were isolated from human faeces. Cells of strain YIT 11850(T) were coccobacilli, asaccharolytic and largely unreactive, with only traces of lactate and propionate as metabolic end products; however, strain YIT 11850(T) was able to decarboxylate succinate to propionate. The DNA G+C content of strain YIT 11850(T) was 51.9 mol%. Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to Dialister propionicifaciens, with 95.1 % sequence similarity between the two taxa. Biochemical data supported the affiliation of strain YIT 11850(T) to the genus Dialister. Strain YIT 11850(T) therefore represents a novel species for which the name Dialister succinatiphilus sp. nov. is proposed; the type strain is YIT 11850(T) (=DSM 21274(T)=JCM 15077(T)). Cells of the other isolate, strain YIT 11860(T), were non-motile, rod-shaped, positive for aesculin hydrolysis, negative for indole production, produced succinic and acetic acids as end products of glucose metabolism and possessed a DNA G+C content of 45.5 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family 'Porphyromonadaceae' related to Barnesiella viscericola (96.0 %); similarity values with species within the family 'Porphyromonadaceae' with validly published names were less than 86 %. Biochemical data supported the affiliation of strain YIT 11860(T) to the genus Barnesiella. Strain YIT 11860(T) therefore represents a novel species for which the name Barnesiella intestinihominis sp. nov. is proposed; the type strain is YIT 11860(T) (=DSM 21032(T)=JCM 15079(T)).


Subject(s)
Bacteroidetes/classification , Bacteroidetes/physiology , Feces/microbiology , Veillonellaceae/classification , Veillonellaceae/physiology , Bacteroidetes/genetics , Humans , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Species Specificity , Veillonellaceae/genetics
13.
Int J Syst Evol Microbiol ; 58(Pt 4): 970-5, 2008 Apr.
Article in English | MEDLINE | ID: mdl-18398204

ABSTRACT

Three strains of anaerobic, non-spore-forming, Gram-negative coccobacilli (YIT 11816T, YIT 11817 and YIT 11818) were isolated from human faeces. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the family Alcaligenaceae and to be related to the type strain of Sutterella stercoricanis (94.9 %) and to Sutterella wadsworthensis WAL 7877 (94.3 %); the similarity to strains of any other species with a validly published name within the family Alcaligenaceae was less than 92 %. Biochemical data supported the affiliation of these strains to the genus Sutterella. These strains therefore represent a novel species, for which the name Sutterella parvirubra sp. nov. is proposed; the type strain is YIT 11816T (=DSM 19354T =JCM 14724T). The cells of another isolate, strain YIT 11815T, were non-spore-forming, Gram-negative, very large rods, 1x5-200 microm in size, with or without a central, subterminal or terminal swelling of 2-4 microm diameter when grown in a broth medium supplemented with glucose. Based on comparative 16S rRNA gene sequencing, this bacterium is a member of the family Acidaminococcaceae, and most closely related to Megamonas hypermegale (95.3 % similarity to the type strain). Interestingly, the 16S rRNA gene sequence of strain YIT 11815T showed 99 % similarity to sequences of uncultured colonic bacteria. A 16S rRNA gene sequence divergence value of >3 % from known cultured species suggested that isolate YIT 11815T represents a novel species, for which the name Megamonas funiformis sp. nov. is proposed; the type strain is YIT 11815T (=DSM 19343T =JCM 14723T).


Subject(s)
Alcaligenaceae/classification , Alcaligenaceae/isolation & purification , Veillonellaceae/classification , Veillonellaceae/isolation & purification , Alcaligenaceae/genetics , Alcaligenaceae/metabolism , Base Sequence , DNA Primers/genetics , DNA, Bacterial/genetics , Feces/microbiology , Genes, Bacterial , Humans , Microscopy, Electron, Scanning , Microscopy, Electron, Transmission , Molecular Sequence Data , Phenotype , Phylogeny , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Species Specificity , Terminology as Topic , Veillonellaceae/genetics , Veillonellaceae/metabolism
14.
Biol Pharm Bull ; 31(3): 357-62, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18310892

ABSTRACT

Aromatase, a key steroidogenic enzyme that catalyses the conversion of androgens to estrogens, present a target for endocrine disrupting chemicals. However, little is known about the effect of pollutants on aromatase enzymes. In this study, we first optimized a non-radioisotope aromatase assay using rat ovarian microsomes in vitro and measuring the estrone level with an enzyme-linked immunosorbent assay (EIA method). The sensitivity of the EIA method was about ten times as high as that of the radioisotope (RI) method. A significant positive correlation was indicated between EIA and RI method. We used this EIA assay system to investigate the effects of aromatase activity on 45 chemicals that had previously been reported to act as endocrine disruptors or to have the possibility of having such an effect. Six of the chemicals, rose bengal, erythrosine, phloxine, allura red, gallic acid, and tributyltin, inhibited aromatase activity. The inhibitory effect of rose bengal was the strongest (IC50=2.4 x 10(-8) M), and its strength of inhibition was about 100 times that of a known aromatase inhibitor, 4-hydroxy-androstenedione (IC50=2.6 x 10(-6) M) but was about 1/25 that of fadrazole (IC50=1.0 x 10(-9) M). It is thought that this EIA method would be useful for measuring the aromatase activity of microstructures.


Subject(s)
Aromatase/metabolism , Biosensing Techniques/methods , Endocrine Disruptors/toxicity , Estrone/analysis , Microsomes/enzymology , Ovary/enzymology , Animals , Endocrine Disruptors/chemistry , Enzyme-Linked Immunosorbent Assay , Female , Rats , Sensitivity and Specificity
15.
Biol Pharm Bull ; 31(3): 375-9, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18310895

ABSTRACT

Disposable gloves made of nitrile-butadiene rubber (NBR) are used for contact with foodstuffs rather than polyvinyl chloride gloves containing di(2-ethylhexyl)phthalate (DEHP), because endocrine-disruptive effects are suspected for phthalate diesters including DEHP. However, 4,4'-butylidenebis(6-t-butyl-m-cresol) (BBBC), 2,4-di-t-butylphenol, and 2,2,4-trimetyl-1,3-pentanediol diisobutyrate can be eluted from NBR gloves, and possibly also detected in food. In this study, we examined the endocrine-disrupting effects of these chemicals via androgen receptor (AR) and estrogen receptor (ER)-mediated pathways using stably transfected reporter gene cell lines expressing AR (AR-EcoScreen system) and ER (MVLN cells), respectively. We also examined the binding activities of these chemicals to AR and ER. The IC50 value of BBBC for antagonistic androgen was in the range of 10(-6)M. The strength of inhibition was about 5 times that of a known androgen antagonist, 1,1'-(2,2-dichloroethylidene)bis[4-chlorobenzene] (p,p'-DDE), and similar to that of bisphenol A. The IC50 value of BBBC for antagonistic estrogen was in the range of 10(-6)M. These results suggest that BBBC and its structural homologue, 4,4'-thiobis(6-t-butyl-m-cresol) are androgen and estrogen antagonists. It is therefore necessary to study these chemicals in vivo, and clarify their effect on the endocrine system.


Subject(s)
Butadienes/chemistry , Elastomers/chemistry , Endocrine Disruptors/toxicity , Gene Expression/drug effects , Genes, Reporter , Gloves, Protective/standards , Animals , Binding, Competitive , Biological Assay/methods , CHO Cells , Cricetinae , Cricetulus , Endocrine Disruptors/chemistry , Molecular Structure , Receptors, Androgen/genetics , Receptors, Androgen/metabolism , Receptors, Estrogen/genetics , Receptors, Estrogen/metabolism
16.
Biosci Biotechnol Biochem ; 72(2): 360-7, 2008 Feb.
Article in English | MEDLINE | ID: mdl-18256494

ABSTRACT

This report describes a new immunological method for the detection and quantification of Nitrospira populations using the reverse passive latex agglutination (RPLA). The numbers of the genus Nitrospira have been quantified only by molecular biological techniques such as FISH and quantitative PCR to date. Using high-density latex particles and a specific polyclonal antibody, Nitrospira populations in the wastewater treatment process were quantified in the shortest 4 h of incubation. The minimum detectable number of Nitrospira cells was 7.0x10(5) (log(10) 5.85) cells/ml. It is thought that the RPLA method can quantify Nitrospira populations more simply, economically, and speedily than molecular biological techniques or the culture method, because this procedure has a simple protocol and does not require the use of specialized equipment, expensive reagents, or technical skill. Therefore it is applicable for use in the everyday control and maintenance of water quality in wastewater treatment facilities where equipment is not sufficient or in the field.


Subject(s)
Bacteria/isolation & purification , Latex Fixation Tests/methods , Water Microbiology , Bacteria/genetics , Base Sequence , DNA Primers , In Situ Hybridization, Fluorescence , Polymerase Chain Reaction
17.
Biol Pharm Bull ; 30(12): 2328-33, 2007 Dec.
Article in English | MEDLINE | ID: mdl-18057721

ABSTRACT

We constructed a reproducible, simple, and small-scale determination method of the psychoactive drugs that acted directly on the monoamine receptor by measuring the activation of [(35)S]guanosine-5'-O-(3-thio)-triphosphate binding to guanine nucleotide-binding proteins (G proteins). This method can simultaneously measure the effects of three monoamines, namely dopamine (DA), serotonin (5-HT), and norepinephrine (NE), in rat brain membranes using a 96-well microplate. Activation of D(1) and D(2) receptors in striatal membranes by DA as well as 5-HT and NEalpha(2) receptors in cortical membranes could be measured. Of 12 tested phenethylamines, 2,5-dimethoxy-4-chlorophenethylamine (2C-C), 2,5-dimethoxy-4-ethylphenethylamine (2C-E), and 2,5-dimethoxy-4-iodophenethylamine (2C-I) stimulated G protein binding. The other phenethylamines did not affect G protein binding. All 7 tryptamines tested stimulated G protein binding with the following rank order of potency; 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT)>5-methoxy-N,N-diallyltryptamine (5-MeO-DALT)>5-methoxy-alpha-methyltryptamine (5-MeO-AMT)>or=5-methoxy-N,N-methylisopropyltryptamine (5-MeO-MIPT)>5-methoxy-N,N-diisopropyltryptamine (5-MeO-DIPT)>N,N-dipropyltryptamine (DPT)>or=alpha-methyltryptamine (AMT). This assay system was able to designate psychoactive drugs as prohibited substances in accordance with criteria set forth by the Tokyo Metropolitan government.


Subject(s)
Brain Chemistry/drug effects , Guanosine 5'-O-(3-Thiotriphosphate)/metabolism , Psychotropic Drugs/pharmacology , Allyl Compounds/metabolism , Animals , Cerebral Cortex/drug effects , Cerebral Cortex/metabolism , GTP-Binding Proteins/metabolism , In Vitro Techniques , Male , Membranes/drug effects , Membranes/metabolism , Norepinephrine/metabolism , Phenethylamines/metabolism , Piperazines/metabolism , Rats , Rats, Sprague-Dawley , Serotonin/metabolism , Structure-Activity Relationship , Sulfur Radioisotopes , Tryptamines/metabolism
18.
Int J Syst Evol Microbiol ; 57(Pt 7): 1673-1674, 2007 Jul.
Article in English | MEDLINE | ID: mdl-17625216

ABSTRACT

Megamonas hypermegale is the sole species of the genus Megamonas included in the List of Prokaryotic Names with Standing in Nomenclature and in the databases of DDBJ, EBI/EMBL and NCBI/GenBank it is placed in the lineage of Bacteroidetes; Bacteroidetes (class); 'Bacteroidales'; Bacteroidaceae; Megamonas. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that this species clustered with species of the family 'Acidaminococcaceae' but not with those of the Bacteroidaceae. The genus Megamonas should be placed in the lineage of Firmicutes; Clostridia; Clostridiales; 'Acidaminococcaceae'; Megamonas.


Subject(s)
Bacteroidaceae/classification , Veillonellaceae/classification , Bacteroidaceae/genetics , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Homology, Nucleic Acid , Veillonellaceae/genetics
19.
Eur J Pharmacol ; 559(2-3): 132-7, 2007 Mar 22.
Article in English | MEDLINE | ID: mdl-17223101

ABSTRACT

We developed a reproducible, simple, and small-scale method for determining the re-uptake and release of monoamines (dopamine, serotonin (5-HT) and norepinephrine) using rat brain synaptosomes. These assays were then applied to study the effects of different kinds of non-medically used psychoactive drugs on monoamine re-uptake and release. The phenethylamine derivatives, 4-fluoroamphetamine, 2-methylamino-3,4-methylene-dioxy-propiophenone (methylone), 1-(1,3-benzodioxol-5-yl)-2-butanamine (BDB), and N-methyl-1-(1,3-benzodioxol-5-yl)-2-butanamine (MBDB), had strong inhibitory effects on the re-uptake of dopamine, 5-HT and norepinephrine. 4-Fluoroamphetamine, methylone and BDB also strongly increased the release of the three monoamines, but MBDB increased 5-HT and norepinephrine release, but had little effect on dopamine release. However, 2,5-dimethoxy-4-iodophenethylamine (2C-I), 2,5-dimethoxy-4-ethylphenethylamine (2C-E), 2,5-dimethoxy-4-chlorophenethylamine (2C-C), 2,4,5-trimethoxyamphetamine (TMA-2) and 2,4,6-trimethoxyamphetamine (TMA-6), which are methoxylated phenethylamine derivatives, slightly influenced the re-uptake and release of monoamines. Alpha-metyltryptamine (AMT), a tryptamine derivative, was one of the strongest re-uptake inhibitors and releasers of the three monoamines. The tryptamine derivative, 5-methoxy-alpha-methyltryptamine (5-MeO-AMT), also strongly inhibited re-uptake and increased the release of the three monoamines. N,N-dipropyltryptamine (DPT), 5-methoxy-N,N-diisopropyltryptamine (5-MeO-DIPT), 5-methoxy-N,N-methylisopropyltryptamine (5-MeO-MIPT), and 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) inhibited monoamine re-uptake, but had a few effects on monoamine release. 1-(3-Chlorophenyl)piperazine (3CPP) and 1-(methoxyphenyl)piperazine (4MPP), which are piperazine derivatives, inhibited monoamine re-uptake and accelerated their release. The results suggest that some designer drugs strongly act on the central nerve system to the same extent as restricted drugs.


Subject(s)
Biogenic Monoamines/metabolism , Brain/drug effects , Designer Drugs/pharmacology , Psychotropic Drugs/pharmacology , Synaptic Transmission/drug effects , Adrenergic Uptake Inhibitors/pharmacology , Animals , Biological Assay/methods , Brain/metabolism , Dopamine/metabolism , Dopamine Uptake Inhibitors/pharmacology , Dose-Response Relationship, Drug , In Vitro Techniques , Male , Norepinephrine/metabolism , Rats , Rats, Sprague-Dawley , Reproducibility of Results , Serotonin/metabolism , Selective Serotonin Reuptake Inhibitors/pharmacology , Synaptosomes/drug effects , Synaptosomes/metabolism
20.
Exp Biol Med (Maywood) ; 232(2): 301-8, 2007 Feb.
Article in English | MEDLINE | ID: mdl-17259338

ABSTRACT

Styrene trimers migrate from polystyrene food container into foods. We evaluated the estrogenic activity of styrene trimers such as 2,4,6-triphenyl-1-hexene (ST-1), 1a-phenyl-4a-(1'-phenylethyl)tetralin (ST-2), 1a-phenyl-4e-(1'-phenylethyl)tetralin(ST-3), 1e-phenyl-4a-(1'-phenylethyl)tetralin (ST-4), and 1e-phenyl-4e-(1'-phenylethyl)tetralin (ST-5) using the reporter-gene assay with MVLN cells stably expressing the estrogen-stimulated reporter gene, and it was confirmed that ST-1, ST-3, and ST-4 had estrogen-like activity. On the other hand, ST-2 and ST-5 had anti-estrogen-like activity. We examined the estrogenic activity in vivo of ST-1, ST-3, and ST-4. The styrene trimers were administered to pregnant rats, and the effects on the offspring were examined. ST-1, ST-3, or ST-4 (0, 10, 100, 1000 microg/kg body wt/day) were subcutaneously injected into pregnant rats from gestational Day 11 through 17, and the male offspring were sacrificed on postnatal days (PND) 101-103. In the ST-4 treatment groups, the relative anogenital distance on PND 3 was significantly shortened. The relative testis weight was remarkably decreased in all styrene trimer treatment groups. Relative weights of the prostate and epididymides significantly decreased in the ST-4 treatment groups. The relative brain weight was markedly reduced in the ST-3 and ST-4 treatment groups. A significant decrease of the Sertoli cell count was observed in the ST-1 and ST-4 treatment groups. The serum follicle stimulating hormone level was remarkably reduced in all styrene trimer treatment groups. The luteinizing hormone level was significantly decreased and the testosterone level increased in the ST-1 and ST-4 groups. These results suggest that prenatal exposure to estrogenic styrene trimers at low levels obstructed genital organ development, and disrupted the endocrine systems of male rat offspring.


Subject(s)
Genitalia, Male/drug effects , Maternal Exposure , Styrene/pharmacology , Animals , Female , Male , Polymers , Pregnancy , Rats , Rats, Sprague-Dawley , Styrene/chemistry
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